Abstract
Proteomics has become an attractive science in the postgenomic era, given its capacity to identify up to thousands of molecules in a single, complex sample and quantify them in an absolute and/or relative manner. The use of these techniques enables understanding of cellular and molecular mechanisms of diseases and other biological conditions, as well as identification and screening of protein biomarkers. Here we provide a straightforward, up-to-date compilation and comparison of the main quantitation techniques used in comparative proteomics such as in vitro and in vivo stable isotope labeling and label-free techniques. Additionally, this chapter includes common methods for data acquisition in proteomics and some appropriate methods for data processing. This compilation can serve as a reference for scientists who are new to, or already familiar with, quantitative proteomics.
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Abbreviations
- AIF:
-
All-ion fragmentation
- AQUA:
-
Absolute quantification
- CAD:
-
Collision-activated dissociation
- CE:
-
Collision energy
- DDA:
-
Data-dependent acquisition
- DIA:
-
Data-independent acquisition
- dNSAF:
-
Distributed normalized spectral abundance factor
- emPAI:
-
Exponentially modified protein abundance index
- FT-ARM:
-
Fourier transform-all reaction monitoring
- HDMSE:
-
High-definition MSE
- iBAQ:
-
Intensity-based absolute quantification
- ICPL:
-
Isotope-coded protein label
- IMS:
-
Ion mobility separation
- LRP:
-
Labeled reference peptide
- MRM:
-
Multiple reaction monitoring
- MSE:
-
DIA method from Waters Co.
- MSX:
-
Multiplexed MS/MS
- mTRAQ:
-
Mass-differential tags for relative and absolute quantitation
- NSAF:
-
Normalized spectral abundance factor
- PSAQ:
-
Protein standard absolute quantification
- pSILAC:
-
Pulsed stable isotope labeling of amino acids in cell culture
- QconCAT:
-
Quantitative concatemers
- QQQ:
-
Triple quadrupole
- SID:
-
Standard isotope dilution
- SILAM:
-
Stable isotope labeling of amino acids in mammals
- SILIP:
-
Stable isotope labeling in planta
- SIN:
-
Normalized spectral index
- SPS-MS3:
-
Synchronous precursor selection MS/MS/MS
- TMT:
-
Tandem mass tags
- UDMSE:
-
Ultra-definition MSE
- XDIA:
-
Extended data-independent acquisition
- XIC:
-
Extracted ion chromatogram
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Acknowledgments
BJS, MF, and DMS would like to thank FAPESP for funding (under grant numbers2016/07948-8, 2016/18715-4, and 2013/08711-3).
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The authors declare no conflict of interest.
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Smith, B.J., Martins-de-Souza, D., Fioramonte, M. (2019). A Guide to Mass Spectrometry-Based Quantitative Proteomics. In: Guest, P. (eds) Pre-Clinical Models. Methods in Molecular Biology, vol 1916. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8994-2_1
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